Taxonomic revision reveals potential impacts of Black Summer megafires on a cryptic species

2022 ◽  
Author(s):  
Chris J. Jolly ◽  
Harry A. Moore ◽  
Mitchell A. Cowan ◽  
Teigan Cremona ◽  
Judy A. Dunlop ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Taxonomic Revision

scholarly journals Co-occurring cryptic species pose challenges for conservation: a case study of the African dwarf crocodile (Osteolaemusspp.) in Cameroon

Oryx ◽  
2014 ◽  
Vol 49 (4) ◽  
pp. 584-590 ◽  
Author(s):  
Nicole L. Smolensky
Keyword(s):  
Cryptic Species ◽  
Conservation Status ◽  
Taxonomic Revision ◽  
Single Species ◽  
Conservation Strategies ◽  
Encounter Rates ◽  
Distribution Maps ◽  
Species Complexes ◽  
Threatened Taxa ◽  
Population Structures

AbstractThe conservation status of threatened taxa may be obfuscated by the detection of cryptic species complexes, in both vertebrate and invertebrate species. African dwarf crocodiles (Osteolaemusspp.) are hunted throughout their range but their conservation status is unknown. Few population assessments have been carried out and there has been a taxonomic revision of the number of species in the genus. The similar morphologies ofOsteolaemus tetraspisandOsteolaemus osbornipose a challenge for conservation in Cameroon, where they are still managed as a single species. Nocturnal spotlight surveys were conducted in three regions during August–November 2010 and December 2011–February 2012 to provide population assessments ofO. tetraspisandO. osborniand raise awareness of the two species in Cameroon. The mean encounter rates ofO. tetraspisandO. osborniwere 1.02 ± SD 1.34 (65 individuals in 39 surveys) and 0.61 ± SD 0.38 (three in four surveys) crocodiles per km, respectively. TheO. tetraspispopulation comprised juveniles predominantly and had a male-biased sex ratio. The fewO. osbornidetected comprised both adults and juveniles. Both species are threatened in Cameroon, based on low encounter rates, young population structures and the threats of habitat loss and hunting pressure. This study provides distribution maps and serves as a baseline to quantify population trends and inform conservation strategies.

Revision of the Parmelia saxatilis group in Italy based on morphological, chemical, and molecular data

Phytotaxa ◽  
2021 ◽  
Vol 512 (1) ◽  
Author(s):  
MARIA BEATRICE CASTELLANI ◽  
ELISABETTA BIANCHI ◽  
ANDREA COPPI ◽  
JURI NASCIMBENE ◽  
RENATO BENESPERI
Keyword(s):  
Genetic Diversity ◽  
Cryptic Species ◽  
Taxonomic Revision ◽  
Molecular Data ◽  
Species Level ◽  
Widespread Species ◽  
Italian Peninsula ◽  
Combined Use ◽  
Molecular Studies ◽  
Shed Light

Recent molecular studies on Parmelia revealed several new semi-cryptic and cryptic species, suggesting the existence of considerable genetic diversity within this genus that may not yet be expressed at the phenotypic level. This is the case of the two species Parmelia ernstiae and P. serrana that have been described in the P. saxatilis group from Europe and that are still poorly known in Italy. The main aim of this study is to shed light into the Italian distribution of these cryptic species on the basis of a systematic and taxonomic revision of exiccata and new specimens of the Parmelia saxatilis group collected along a biogeographical gradient through the Italian peninsula. In this revision, we combined morphological, chemical, and molecular data and evaluated their reliability for identification at the species level. Results indicate that P. saxatilis is the most widespread species and that P. ernstiae is much more widespread than previously thought. In contrast, P. serrana seems to be a rare species in Italy. Our results also indicate that the combined use of morphological and chemical data does not provide a reliable tool to discriminate the cryptic species of this group and that molecular data are thus indispensable for identification at the species level. Finally, our phylogenetic analysis supports the existence of an unrecognized diversity in parmelioid lichens that should be further investigated.

scholarly journals A morphometric assessment of species boundaries in a widespread anole lizard (Squamata: Dactyloidae)

2020 ◽  
Vol 130 (4) ◽  
pp. 813-825
Author(s):  
Tanner C Myers ◽  
Pietro L H de Mello ◽  
Richard E Glor
Keyword(s):  
Cryptic Species ◽  
Model Fitting ◽  
Taxonomic Revision ◽  
Genetic Data ◽  
Morphological Data ◽  
Species Boundaries ◽  
Morphometric Data ◽  
Normal Mixture ◽  
Test Species ◽  
Candidate Species

Abstract Cryptic species – genetically distinct species that are morphologically difficult to distinguish – present challenges to systematists. Operationally, cryptic species are very difficult to identify and sole use of genetic data or morphological data can fail to recognize evolutionarily isolated lineages. We use morphometric data to test species boundaries hypothesized with genetic data in the North Caribbean bark anole (Anolis distichus), a suspected species complex. We use univariate and multivariate analyses to test if candidate species based on genetic data can be accurately diagnosed. We also test alternative species delimitation scenarios with a model fitting approach that evaluates normal mixture models capable of identifying morphological clusters. Our analyses reject the hypothesis that the candidate species are diagnosable. Neither uni- nor multivariate morphometric data distinguish candidate species. The best-supported model included two morphological clusters; however, these clusters were uneven and did not align with a plausible species divergence scenario. After removing two related traits driving this result, only one cluster was supported. Despite substantial differentiation revealed by genetic data, we recover no new evidence to delimit species and refrain from taxonomic revision. This study highlights the importance of considering other types of data along with molecular data when delimiting species.

Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919, (Anura: Dicroglossidae)

Zootaxa ◽  
2020 ◽  
Vol 4869 (4) ◽  
pp. 451-492
Author(s):  
SAMADHAN PHUGE ◽  
AJINKYA BHARATRAJ PATIL ◽  
RADHAKRISHNA PANDIT ◽  
NIRMAL U KULKARNI ◽  
B.H. CHENNAKESHAVAMURTHY ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Dna Sequences ◽  
Taxonomic Revision ◽  
Genetic Data ◽  
Type Specimen ◽  
Dominant Frequency ◽  
Dorsal Side ◽  
Type Locality ◽  
Rrna Gene ◽  
Type Specimens

Frogs of the genus Minervarya are cryptic and widely distributed in South Asia. However, many of them lack information about the precise type locality, genetic data, and distribution range. The present study aimed to examine the genetic affinities of a widely distributed species Minervarya syhadrensis around its type locality in the northern Western Ghats (Pune, Maharashtra). We studied the type specimen of M. syhadrensis and collected similar sized Minervarya frogs from Pune district. In the field, we observed two different calls from morphologically similar (M. syhadrensis like) males suggesting the sympatric occurrence of two cryptic species (that we initially named Minervarya species A and Minervarya species B). We analyzed morphology, call pattern, and mitochondrial 16S rRNA gene sequence of both species. Minervarya species A has a long call with a low pulse repetition rate and higher dominant frequency compared to that of the Minervarya species B. These species cannot be differentiated based on morphometric data. However, they can be sorted out using morphological characters such as the presence of longitudinal skin folds on the dorsal side (Minervarya species A) and differences in foot webbing. DNA sequences of Minervarya species A and Minervarya species B are matching with those of M. caperata and M. agricola respectively. After studying the type specimens of M. syhadrensis and M. caperata, we found morphological similarities (longitudinal skin folds) with the samples of Minervarya species A collected during the present study. Based on the results of our study (morphology and genetic) and available literature, we propose to redefine M. syhadrensis as applying to the lineage initially named Minervarya species A, and to treat the species M. caperata as a junior synonym of M. syhadrensis. Our study will be helpful in further taxonomic revision of the genus, and provides natural history information for M. syhadrensis and M. agricola.  

scholarly journals Molecular taxonomy of endemic coastal Ligia isopods from the Hawaiian Islands: re-description of L. hawaiensis and description of seven novel cryptic species

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7531
Author(s):  
Carlos A. Santamaria
Keyword(s):  
Cryptic Species ◽  
Species Delimitation ◽  
Molecular Taxonomy ◽  
Hawaiian Islands ◽  
Nuclear Gene ◽  
Morphological Differentiation ◽  
Taxonomic Revision ◽  
Hawaiian Archipelago ◽  
Genetic Lineages ◽  
Molecular Characters

Past phylogeographic work has shown Ligia hawaiensis, a coastal isopod species endemic to the Hawaiian Islands, to be a paraphyletic complex of several highly genetically divergent yet morphologically cryptic lineages. Despite the need for a taxonomic revision of this species, the lack of morphological differentiation has proven an impediment to formally describe new Ligia species in the region. Molecular characters and species delimitation approaches have been successfully used to formally describe cryptic species in other crustacean taxa, suggesting they may aid taxonomic revisions of L. hawaiensis. Herein, various distance- and tree-based molecular species delimitation approaches are applied on a concatenated dataset comprised of both mitochondrial and nuclear gene sequences of L. hawaiensis and L. perkinsi, a terrestrial species endemic to the Hawaiian archipelago. Results of these analyses informed a taxonomic revision leading to the redescription of L. hawaiensis and the description of seven new cryptic species on the basis of molecular characters: L. dante, L. eleluensis, L. honu, L. kamehameha, L. mauinuiensis, L. pele, and L. rolliensis. These coastal Ligia species from the Hawaiian archipelago appear to be largely limited to single islands, where they appear largely constrained to volcanic rift zones suggesting allopatric events at local scales may drive diversification for poorly dispersing organisms in the Hawaiian coastlines. Additional work remains needed to fully assess the role of said events; however, the description of these novel species underscore their potential to aid in studies of local diversification of marine organisms in Hawai‘i. Lastly, this represents the first application of molecular taxonomic approaches to formally describe genetic lineages found in Ligia isopods as species, underscoring the promise these methods hold to taxonomic revisions in other species in the genus shown to harbor cryptic genetic lineages.

An allozyme study of the blue swimmer crab, Portunus pelagicus (Crustacea : Portunidae), in Australia: stock delineation in southern Australia and evidence for a cryptic species in northern waters

1999 ◽  
Vol 50 (1) ◽  
pp. 15 ◽  
Author(s):  
Simon R. Bryars ◽  
Mark Adams
Keyword(s):  
Cryptic Species ◽  
Goodness Of Fit ◽  
South Australia ◽  
Taxonomic Revision ◽  
Allozyme Variation ◽  
Northern Territory ◽  
Portunus Pelagicus ◽  
The Common ◽  
Population Substructuring ◽  
F Statistics

Allozyme analysis was used to examine the species-level systematics and stock structure of the Australian blue swimmer crab Portunus pelagicus. Fifty-seven crabs from eight sites were screened in an overview study for allozyme variation at 35 loci. This overview study revealed the presence of two species, differing at a Nei D of 0.14 (2% fixed differences), in the Darwin region of northern Australia. One of these species corresponds to the common P. pelagicus found throughout Australia, whereas the other is most likely either an undescribed ‘cryptic’ species, or the east-Asian species P. trituberculatus. In total, 609 P. pelagicus from 11 sites covering three regions in South Australia and two regions in the Northern Territory were then genotyped at seven polymorphic loci and these data assessed, using goodness- of-fit and F-statistics, for the existence of subpopulations. Four discrete subpopulations could be discerned, namely West Coast, Spencer Gulf, and Gulf St Vincent in South Australia, and Darwin–Gove in the Northern Territory. No evidence of population substructuring among sites within each subpopulation was evident from the allozyme data. The results support the current recognition of the three South Australian regions as separate stocks, and suggest that a taxonomic revision of Indo-Pacific Portunus is warranted.

scholarly journals Genetic, bioacoustic and morphological analyses reveal cryptic speciation in the warbling vireo complex (Vireo gilvus: Vireonidae: Passeriformes)

2021 ◽  
Author(s):  
Amanda M Carpenter ◽  
Brendan A Graham ◽  
Garth M Spellman ◽  
John Klicka ◽  
Theresa M Burg
Keyword(s):  
Cryptic Species ◽  
Ecological Niche Modeling ◽  
Taxonomic Revision ◽  
Black Hills ◽  
Separate Species ◽  
Phenotypic Data ◽  
Eastern Group ◽  
Long Period ◽  
Genetic Groups ◽  
Group A

Cryptic species are closely related taxa that are difficult to separate morphologically, but are reproductively isolated. Here we examine the warbling vireo complex (Vireo gilvus), a widespread songbird speculated to be comprised of more than one cryptic species. We included three taxa within the complex: two of the western (Vireo gilvus swainsonii and Vireo gilvus brewsteri) subspecies and the single eastern (Vireo gilvus gilvus) subspecies. We used mtDNA and microsatellite loci to assess the congruence of genetic data to the current subspecies boundaries. We then incorporated bioacoustic, morphometric, and ecological niche modeling analyses to further examine differences. We found two genetic groups with mtDNA analysis. Microsatellite analyses revealed four genetic groups: an eastern group, a Black Hills group and two western groups that do not agree with current western subspecies boundaries based on phenotypic data. Our results suggest that eastern and western warbling vireos have been reproductively isolated for a long period of time and therefore, may be best treated as separate species; however, more research into areas of contact to examine the presence of hybridization is advised before making a taxonomic revision. Differences between the two western genetic groups appear less clear, requiring additional research.

scholarly journals Multilocus phylogeny and cryptic diversity of white-toothed shrews (Mammalia, Eulipotyphla, Crocidura) in China

2019 ◽  
Author(s):  
Shunde Chen ◽  
Jiao Qing ◽  
Zhu Liu ◽  
Yang Liu ◽  
Mingkun Tang ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Mitochondrial Gene ◽  
Time Estimation ◽  
Taxonomic Revision ◽  
Early Pleistocene ◽  
Taxon Sampling ◽  
Cryptic Diversity ◽  
Divergence Time Estimation ◽  
Late Pliocene ◽  
Putative Species

Abstract Background: Crocidura, the most speciose mammalian genus, occurs across much of Asia, Europe and Africa. In China, the taxonomy has been primarily based on cursory morphological comparisons and molecular phylogenetic relationships of the genus remain unexplored. In order to understand the phylogeny of this group in China, we estimated the first multi-loci phylogeny and conducted species delimitation, including taxon sampling throughout their distribution range.Results: We obtained one mitochondrial gene (~ 1, 134 bp) and three nuclear genes (~ 2, 170 bp) for 132 samples from 57 localities. Molecular analyses identified at least 14 putative species that occur within two major well-supported groups in China. Polyphyletic C. wuchihensis appears to be composed of two putative species. Two subspecies, C. rapax rapax and C. rapax kurodai should be elevated to full species status. A phylogenetic tree based on mitochondrial gene from Asian Crocidura species showed that C. rapax rapax was found embedded within C. attenuate, making the latter a paraphyletic group. Three strongly supported cryptic species are revealed from Motuo of Xizang, Zada of Xizang, Hunan and Zhejiang. The divergence time estimation suggested that China’s Crocidura species began to diversify during the late Pliocene (3.70 Ma) and the Early Pleistocene (2.33 Ma) periods, followed by a series of diversifications through the Pleistocene period.Conclusions: The cryptic diversity found in this study indicated that the number of species is strongly underestimated under the current taxonomy. We propose that the three cryptic species should be evaluated using extensive taxon sampling and comprehensive morphological and morphometric approaches. Climate change since the late Pliocene periods and the uplift of the Himalayas may have resulted in the diversification and speciation of China’s Crocidura species. In short, the underestimated diversity underlines the need for a taxonomic revision of China’s Crocidura species.

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